Objectives To investigate the effectiveness of a two-stage evaluation for selecting individuals for chronic disease lifestyle guidance. Design Cross-sectional study. Setting The specific subjects of this report are evaluation of disease or risk associated with metabolic syndrome, a condition for which this type of two-stage evaluation may be particularly useful. Participants The subjects were 648 men and women who participated in a health evaluation and promotion program between April 2007 and October 2007. Results The results of the primary prevention assessments are as follows: Among men, there was little difference between the proportions who met the metabolic syndrome criteria in Japan (14%) and the insulin resistance criteria (17%) ; however, the proportion who met the original criteria was considerably greater (44%) . Some individuals were excluded based on the metabolic syndrome criteria in Japan even though pathological insulin resistance was clearly present. Conclusions When health protection aimed primarily at chronic disease is implemented in a health evaluation and promotion program, secondary and primary prevention should be clearly distinguished, as should group health and individual health. Our comprehensive health evaluation system, which was developed based on these principles, was very useful for implementing health management for individuals in a health evaluation and promotion program.